xgi-org · nwlandry · Nov 2, 2023 · Oct 27, 2023 · Oct 27, 2023 · Oct 27, 2023
diff --git a/.gitignore b/.gitignore
@@ -143,7 +143,6 @@ cython_debug/
 
 # test files
 test.*
-tutorials/test.*
 /.vscode
 
 # airspeed velocity files

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -9,7 +9,7 @@ version: 2
 build:
   os: ubuntu-20.04
   tools:
-    python: "3.9"
+    python: "3.12"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -8,7 +8,6 @@ include CITATION.cff
 include CODE_OF_CONDUCT.md
 include pytest.ini
 
-recursive-include tutorials *.ipynb
 recursive-include logo *.pdf *.png *.svg
 recursive-include requirements *.txt *.md
 

diff --git a/README.md b/README.md
@@ -62,7 +62,7 @@ pip install -e .\[all\]
 
 
 ## Getting Started
-To get started, take a look at the [tutorials](/tutorials/) illustrating the library's basic functionality.
+To get started, take a look at the [tutorials](https://xgi.readthedocs.io/en/stable/api/tutorials.html) illustrating the library's basic functionality.
 
 
 ## Corresponding Data

diff --git a/docs/source/about.rst b/docs/source/about.rst
@@ -27,8 +27,8 @@ mind.
 - Repository: https://github.com/xgi-org/xgi
 - PyPI: `latest release <https://pypi.org/project/xgi/>`_
 - Twitter: `@xginets <https://twitter.com/xginets>`_
-- Contributors: `list <contributors.html>`_
-- Projects using XGI: `list <using-xgi.html>`_
+- `List of Contributors <contributors.html>`_
+- `Projects Using XGI <using-xgi.html>`_
 
 Sign up for our `mailing list <http://eepurl.com/igE6ez>`_ and follow XGI on `Twitter <https://twitter.com/xginets>`_ or `Mastodon <https://mathstodon.xyz/@xginets>`_!
 
@@ -78,9 +78,9 @@ Contributing
 ============
 
 If you want to contribute to this project, please make sure to read the
-`contributing guidelines <HOW_TO_CONTRIBUTE.md>`_.
+`contributing guidelines <https://github.com/xgi-org/xgi/blob/main/HOW_TO_CONTRIBUTE.md>`_.
 We expect respectful and kind interactions by all contributors and users
-as laid out in our `code of conduct <CODE_OF_CONDUCT.md>`_.
+as laid out in our `code of conduct <https://github.com/xgi-org/xgi/blob/main/CODE_OF_CONDUCT.md>`_.
 
 The XGI community always welcomes contributions, no matter how small.
 We're happy to help troubleshoot XGI issues you run into,
@@ -92,9 +92,8 @@ Some concrete ways that you can get involved:
 * **Get XGI updates** by following the XGI `Twitter <https://twitter.com/xginets>`_ account, signing up for our `mailing list <http://eepurl.com/igE6ez>`_, or starring this repository.
 * **Spread the word** when you use XGI by sharing with your colleagues and friends.
 * **Request a new feature or report a bug** by raising a `new issue <https://github.com/xgi-org/xgi/issues/new>`_.
-* **Create a Pull Request (PR)** to address an `open issue <../../issues>`_ or add a feature.
+* **Create a Pull Request (PR)** to address an `open issue <https://github.com/xgi-org/xgi/issues>`_ or add a feature.
 * **Join our Zulip channel** to be a part of the `daily goings-on of XGI <https://xgi.zulipchat.com/join/7agfwo7dh7jo56ppnk5kc23r/>`_.
-.
 
 
 Funding

diff --git a/docs/source/api/convert/xgi.convert.higher_order_network.rst b/docs/source/api/convert/xgi.convert.higher_order_network.rst
@@ -7,6 +7,6 @@ xgi.convert.higher_order_network
 
    .. rubric:: Functions
 
-   .. autofunction:: convert_to_hypergraph
-   .. autofunction:: convert_to_dihypergraph
-   .. autofunction:: convert_to_simplicial_complex
+   .. autofunction:: to_hypergraph
+   .. autofunction:: to_dihypergraph
+   .. autofunction:: to_simplicial_complex
diff --git a/docs/source/api/stats.rst b/docs/source/api/stats.rst
@@ -17,10 +17,10 @@ stats package
       ~xgi.stats.nodestats.clique_eigenvector_centrality
       ~xgi.stats.nodestats.clustering_coefficient
       ~xgi.stats.nodestats.degree
-      ~xgi.stats.nodestats.eigenvector_centrality
+      ~xgi.stats.nodestats.h_eigenvector_centrality
       ~xgi.stats.nodestats.local_clustering_coefficient
       ~xgi.stats.nodestats.node_edge_centrality
-      ~xgi.stats.nodestats.two_nodes_clustering_coefficient
+      ~xgi.stats.nodestats.two_node_clustering_coefficient
 
    *Statistics of edges*
 

diff --git a/docs/source/api/tutorials/Tutorial 8 - Directed Hypergraphs.ipynb b/docs/source/api/tutorials/Tutorial 8 - Directed Hypergraphs.ipynb
diff --git a/docs/source/api/tutorials/XGI in 5 minutes.ipynb b/docs/source/api/tutorials/XGI in 5 minutes.ipynb
@@ -140,7 +140,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "XGI also offers several ways to personalize your plots for higher-order structures. For more options, explore the [focus tutorial on plotting](https://xgi.readthedocs.io/en/stable/api/main/tutorials/Tutorial%205%20-%20Plotting.html) or consult the [documentation](https://xgi.readthedocs.io/en/stable/api/drawing.html).\n",
+    "XGI also offers several ways to personalize your plots for higher-order structures. For more options, explore the [focus tutorial on plotting](https://xgi.readthedocs.io/en/stable/api/tutorials/Tutorial%205%20-%20Plotting.html) or consult the [documentation](https://xgi.readthedocs.io/en/stable/api/drawing.html).\n",
     "\n",
     "For example, you can place the nodes on a circle:"
    ]
@@ -400,7 +400,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.13"
+   "version": "3.10.0"
   },
   "toc": {
    "base_numbering": 1,

diff --git a/docs/source/api/tutorials/quickstart.ipynb b/docs/source/api/tutorials/quickstart.ipynb
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -73,8 +73,8 @@ mind.
 - Repository: https://github.com/xgi-org/xgi
 - PyPI: `latest release <https://pypi.org/project/xgi/>`_
 - Twitter: `@xginets <https://twitter.com/xginets>`_
-- Contributors: `list <contributors.html>`_
-- Projects using XGI: `list <using-xgi.html>`_
+- `List of Contributors <contributors.html>`_
+- `Projects Using XGI <using-xgi.html>`_
 
 Sign up for our `mailing list <http://eepurl.com/igE6ez>`_ and follow XGI on `Twitter <https://twitter.com/xginets>`_ or `Mastodon <https://mathstodon.xyz/@xginets>`_!
 
@@ -113,9 +113,9 @@ Contributing
 ============
 
 If you want to contribute to this project, please make sure to read the
-`contributing guidelines <HOW_TO_CONTRIBUTE.md>`_.
+`contributing guidelines <https://github.com/xgi-org/xgi/blob/main/HOW_TO_CONTRIBUTE.md>`_.
 We expect respectful and kind interactions by all contributors and users
-as laid out in our `code of conduct <CODE_OF_CONDUCT.md>`_.
+as laid out in our `code of conduct <https://github.com/xgi-org/xgi/blob/main/CODE_OF_CONDUCT.md>`_.
 
 The XGI community always welcomes contributions, no matter how small.
 We're happy to help troubleshoot XGI issues you run into,
@@ -127,7 +127,7 @@ Some concrete ways that you can get involved:
 * **Get XGI updates** by following the XGI `Twitter <https://twitter.com/xginets>`_ account, signing up for our `mailing list <http://eepurl.com/igE6ez>`_, or starring this repository.
 * **Spread the word** when you use XGI by sharing with your colleagues and friends.
 * **Request a new feature or report a bug** by raising a `new issue <https://github.com/xgi-org/xgi/issues/new>`_.
-* **Create a Pull Request (PR)** to address an `open issue <../../issues>`_ or add a feature.
+* **Create a Pull Request (PR)** to address an `open issue <https://github.com/xgi-org/xgi/issues>`_ or add a feature.
 * **Join our Zulip channel** to be a part of the `daily goings-on of XGI <https://xgi.zulipchat.com/join/7agfwo7dh7jo56ppnk5kc23r/>`_.
 
 How to Cite
@@ -139,21 +139,23 @@ You can cite XGI either by going to our repository page
 `repository page <https://github.com/xgi-org/xgi>`_ and
 clicking the "cite this repository" button on the right sidebar (which will generate
 a citation in your preferred format) or by copying the following BibTeX entry:
-```
-@article{Landry_XGI_2023,
-    author = {Landry, Nicholas W. and Lucas, Maxime and Iacopini, Iacopo and Petri, Giovanni and Schwarze, Alice and Patania, Alice and Torres, Leo},
-    title = {{XGI: A Python package for higher-order interaction networks}},
-    doi = {10.21105/joss.05162},
-    journal = {Journal of Open Source Software},
-    publisher = {The Open Journal},
-    year = {2023},
-    month = may,
-    volume = {8},
-    number = {85},
-    pages = {5162},
-    url = {https://joss.theoj.org/papers/10.21105/joss.05162},
-}
-```
+
+.. code:: text
+
+  @article{Landry_XGI_2023,
+  author = {Landry, Nicholas W. and Lucas, Maxime and Iacopini, Iacopo and Petri, Giovanni and Schwarze, Alice and Patania, Alice and Torres, Leo},
+  title = {{XGI: A Python package for higher-order interaction networks}},
+  doi = {10.21105/joss.05162},
+  journal = {Journal of Open Source Software},
+  publisher = {The Open Journal},
+  year = {2023},
+  month = may,
+  volume = {8},
+  number = {85},
+  pages = {5162},
+  url = {https://joss.theoj.org/papers/10.21105/joss.05162},
+  }
+
 
 Academic References
 ===================

diff --git a/long_description.rst b/long_description.rst
@@ -30,7 +30,7 @@ To install this package locally:
 
 Getting Started
 ---------------
-To get started, take a look at the `tutorials <https://github.com/xgi-org/xgi/tree/main/tutorials>`_
+To get started, take a look at the `tutorials <https://xgi.readthedocs.io/en/stable/api/tutorials.html>`_
 illustrating the library's basic functionality.
 
 Corresponding Data

diff --git a/tests/convert/test_graph.py b/tests/convert/test_graph.py
@@ -1,15 +1,15 @@
 import xgi
 
 
-def test_convert_to_graph(edgelist2, edgelist5):
+def test_to_graph(edgelist2, edgelist5):
     H1 = xgi.Hypergraph(edgelist2)
     H2 = xgi.Hypergraph(edgelist5)
 
-    G1 = xgi.convert_to_graph(H1)
+    G1 = xgi.to_graph(H1)
     assert set(G1.nodes) == {1, 2, 3, 4, 5, 6}
     assert set(G1.edges) == {(1, 2), (3, 4), (4, 5), (4, 6), (5, 6)}
 
-    G2 = xgi.convert_to_graph(H2)
+    G2 = xgi.to_graph(H2)
     assert set(G2.nodes) == {0, 1, 2, 3, 4, 5, 6, 7, 8}
     assert {frozenset(e) for e in G2.edges} == {
         frozenset({0, 1}),

diff --git a/tests/convert/test_higher_order_network.py b/tests/convert/test_higher_order_network.py
@@ -2,72 +2,72 @@
 
 
 def test_convert_empty_hypergraph():
-    H = xgi.convert_to_hypergraph(None)
+    H = xgi.to_hypergraph(None)
     assert H.num_nodes == 0
     assert H.num_edges == 0
 
 
 def test_convert_empty_dihypergraph():
-    H = xgi.convert_to_dihypergraph(None)
+    H = xgi.to_dihypergraph(None)
     assert H.num_nodes == 0
     assert H.num_edges == 0
 
 
 def test_convert_simplicial_complex_to_hypergraph():
     SC = xgi.SimplicialComplex()
     SC.add_simplices_from([[3, 4, 5], [3, 6], [6, 7, 8, 9], [1, 4, 10, 11, 12], [1, 4]])
-    H = xgi.convert_to_hypergraph(SC)
+    H = xgi.to_hypergraph(SC)
     assert isinstance(H, xgi.Hypergraph)
     assert SC.nodes == H.nodes
     assert SC.edges.members() == H.edges.members()
 
 
 def test_convert_list_to_hypergraph(edgelist2):
-    H = xgi.convert_to_hypergraph(edgelist2)
+    H = xgi.to_hypergraph(edgelist2)
     assert isinstance(H, xgi.Hypergraph)
     assert set(H.nodes) == {1, 2, 3, 4, 5, 6}
     assert H.edges.members() == [{1, 2}, {3, 4}, {4, 5, 6}]
 
 
 def test_convert_pandas_dataframe_to_hypergraph(dataframe5):
-    H = xgi.convert_to_hypergraph(dataframe5)
+    H = xgi.to_hypergraph(dataframe5)
     assert isinstance(H, xgi.Hypergraph)
     assert set(H.nodes) == set(dataframe5["col1"])
     assert H.edges.members() == [{0, 1, 2, 3}, {4}, {5, 6}, {8, 6, 7}]
 
 
 def test_convert_empty_simplicial_complex():
-    S = xgi.convert_to_simplicial_complex(None)
+    S = xgi.to_simplicial_complex(None)
     assert S.num_nodes == 0
     assert S.num_edges == 0
 
 
 def test_convert_hypergraph_to_simplicial_complex():
     H = xgi.Hypergraph()
     H.add_edges_from([[1, 2, 3], [3, 4], [4, 5, 6, 7], [7, 8, 9, 10, 11]])
-    SC = xgi.convert_to_simplicial_complex(H)
+    SC = xgi.to_simplicial_complex(H)
     assert isinstance(SC, xgi.SimplicialComplex)
     assert H.nodes == SC.nodes
     assert H.edges.members() == SC.edges.maximal().members()
 
 
 def test_convert_dihypergraph_to_hypergraph(diedgelist2):
     DH = xgi.DiHypergraph(diedgelist2)
-    H = xgi.convert_to_hypergraph(DH)
+    H = xgi.to_hypergraph(DH)
     assert isinstance(H, xgi.Hypergraph)
     assert H.nodes == DH.nodes
     assert H.edges.members() == [{0, 1, 2}, {1, 2, 4}, {2, 3, 4, 5}]
 
 
 def test_convert_list_to_simplicial_complex(edgelist2):
-    SC = xgi.convert_to_simplicial_complex(edgelist2)
+    SC = xgi.to_simplicial_complex(edgelist2)
     assert isinstance(SC, xgi.SimplicialComplex)
     assert set(SC.nodes) == {1, 2, 3, 4, 5, 6}
     assert SC.edges.maximal().members() == [{1, 2}, {3, 4}, {4, 5, 6}]
 
 
 def test_convert_pandas_dataframe_to_simplicial_complex(dataframe5):
-    SC = xgi.convert_to_simplicial_complex(dataframe5)
+    SC = xgi.to_simplicial_complex(dataframe5)
     assert isinstance(SC, xgi.SimplicialComplex)
     assert set(SC.nodes) == set(dataframe5["col1"])
     assert SC.edges.maximal().members() == [{0, 1, 2, 3}, {4}, {5, 6}, {8, 6, 7}]
diff --git a/xgi/convert/graph.py b/xgi/convert/graph.py
@@ -4,10 +4,10 @@
 
 from ..linalg import adjacency_matrix
 
-__all__ = ["convert_to_graph"]
+__all__ = ["to_graph"]
 
 
-def convert_to_graph(H):
+def to_graph(H):
     """Graph projection (1-skeleton) of the hypergraph H.
     Weights are not considered.
 

diff --git a/xgi/convert/higher_order_network.py b/xgi/convert/higher_order_network.py
@@ -24,13 +24,13 @@
 from .simplex import from_simplex_dict
 
 __all__ = [
-    "convert_to_hypergraph",
-    "convert_to_dihypergraph",
-    "convert_to_simplicial_complex",
+    "to_hypergraph",
+    "to_dihypergraph",
+    "to_simplicial_complex",
 ]
 
 
-def convert_to_hypergraph(data, create_using=None):
+def to_hypergraph(data, create_using=None):
     """Make a hypergraph from a known data structure.
 
     The preferred way to call this is automatically from the class constructor.
@@ -127,7 +127,7 @@ def convert_to_hypergraph(data, create_using=None):
         raise XGIError("Input data has unsupported type.")
 
 
-def convert_to_dihypergraph(data, create_using=None):
+def to_dihypergraph(data, create_using=None):
     """Make a dihypergraph from a known data structure.
 
     The preferred way to call this is automatically from the class constructor.
@@ -184,7 +184,7 @@ def convert_to_dihypergraph(data, create_using=None):
 from ..generators import empty_simplicial_complex
 
 
-def convert_to_simplicial_complex(data, create_using=None):
+def to_simplicial_complex(data, create_using=None):
     """Make a hypergraph from a known data structure.
     The preferred way to call this is automatically
     from the class constructor.
@@ -238,17 +238,17 @@ def convert_to_simplicial_complex(data, create_using=None):
         # edge list
         result = from_hyperedge_list(data, create_using)
         if not isinstance(create_using, SimplicialComplex):
-            return convert_to_simplicial_complex(result)
+            return to_simplicial_complex(result)
 
     elif isinstance(data, pd.DataFrame):
         result = from_bipartite_pandas_dataframe(data, create_using)
         if not isinstance(create_using, SimplicialComplex):
-            return convert_to_simplicial_complex(result)
+            return to_simplicial_complex(result)
 
     elif isinstance(data, dict):
         result = from_simplex_dict(data, create_using)
         if not isinstance(create_using, SimplicialComplex):
-            return convert_to_simplicial_complex(result)
+            return to_simplicial_complex(result)
     elif isinstance(
         data,
         (

diff --git a/xgi/core/dihypergraph.py b/xgi/core/dihypergraph.py
@@ -62,7 +62,7 @@ class DiHypergraph:
     In addition to the methods listed in this page, other methods defined in the `stats`
     package are also accessible via the `DiHypergraph` class.  For more details, see the
     `tutorial
-    <https://github.com/ComplexGroupInteractions/xgi/blob/main/tutorials/Tutorial%206%20-%20Statistics.ipynb>`_.
+    <https://xgi.readthedocs.io/en/stable/api/tutorials/Tutorial%206%20-%20Statistics.html>`_.
 
     References
     ----------
@@ -157,9 +157,9 @@ def __init__(self, incoming_data=None, **attr):
         if incoming_data is not None:
             # This import needs to happen when this function is called, not when it is
             # defined.  Otherwise, a circular import error would happen.
-            from ..convert import convert_to_dihypergraph
+            from ..convert import to_dihypergraph
 
-            convert_to_dihypergraph(incoming_data, create_using=self)
+            to_dihypergraph(incoming_data, create_using=self)
         self._hypergraph.update(attr)  # must be after convert
 
     def __str__(self):